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wwood / finishm

genome improvement and finishing without further sequencing effort
MIT License
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Probes written to temporary file with static name #34

Closed donovan-h-parks closed 9 years ago

donovan-h-parks commented 9 years ago

Hello,

I am trying to run multiple instances of FinishM in parallel. However, I believe the call to velveth fails in this case as it creates a statically named temporary file (/tmp/probes.ftq.gz):

INFO bio-velvet 31/08 07:52:23: Running velveth: /srv/sw/finishm/0.0.3/lib/assembly/../../ext/src/velveth arg13/velvet 51 -fasta -short /tmp/probes.ftq.gz -short ../../seq_data/qc/arg13.qc.1.fq.gz ../../seq_data/qc/arg13.qc.2.fq.gz -create_binary

My runs eventually fail with: ERROR finishm 31/08 00:37:48: Probe sequence #344 has changed - perhaps the wrong velvet assembly directory was specified, or a fresh assembly is required.

Cheers, Donovan

donovan-h-parks commented 9 years ago

Actually, this doesn't seem to be the case. It was just a weird clipping error on my terminal. The probes do have unique names. Still not clear why the run is failing though.

wwood commented 9 years ago

potentially due to non-ATGCN characters in the probe names. Fixed in 0.0.4?

donovan-h-parks commented 9 years ago

This indeed seems to be the issue. Cheers!